Jie Xu

The paper develops a serum-free 6iL/E4 culture system that enables derivation and maintenance of embryonic stem cells (ESCs) across multiple mammalian species, revealing conserved mechanisms for ESC self-renewal.

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

This study identifies subtype-specific epigenomic and 3D genome structures in bladder cancer, linking NPAS2 to luminal subtype regulation and clinical outcomes.

The paper develops a custom ENCODE annotation for cancer genomics, highlighting TF-RBP interactions and network rewiring during oncogenesis, and validates findings using experimental assays.

The paper identifies a correlation between RNA-DNA interactions in normal cells and fusion RNA pairs in cancer, suggesting a mechanism for fusion transcript formation.

The paper introduces a web-based browser for visualizing 3D genome organization and chromatin interactions, enabling integration with other omics data to study gene regulation.

This paper presents an integrative framework to detect structural variants in cancer genomes using multiple methods and finds that non-coding structural variation significantly impacts genome function in cancer cells.

HiCPlus enhances the resolution of Hi-C interaction heatmaps using deep learning, reconstructing high-resolution data from low-resolution inputs.

OMIndel detects large indels using optical map data, outperforming existing tools by reducing false discoveries and identifying indels missed by other technologies.